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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-09-14 15:48:16 UTC
HMDB IDHMDB0001245
Secondary Accession Numbers
  • HMDB01245
Metabolite Identification
Common NamedCDP
DescriptiondCDP, also known as deoxy-CDP, belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O. dCDP is an extremely weak basic (essentially neutral) compound (based on its pKa). dCDP exists in all living species, ranging from bacteria to humans. Within humans, dCDP participates in a number of enzymatic reactions. In particular, dCDP can be biosynthesized from CDP through the action of the enzyme ribonucleoside-diphosphate reductase large subunit. In addition, dCDP can be converted into dCTP; which is mediated by the enzyme nucleoside diphosphate kinase 6. In humans, dCDP is involved in pyrimidine metabolism. Outside of the human body, dCDP has been detected, but not quantified in, several different foods, such as climbing beans, fox grapes, chinese mustards, angelica, and guava. This could make dCDP a potential biomarker for the consumption of these foods. A 2'-deoxycytidine phosphate that is the 2'- deoxy derivative of cytidine 5'-diphosphate (CDP).
Structure
Data?1582752186
Synonyms
ValueSource
2'-Deoxycytidine 5'-diphosphateChEBI
2'-Deoxycytidine diphosphateChEBI
D-1beta-Ribofuranosylcytosine diphosphateChEBI
Deoxycytidine diphosphateChEBI
2'-Deoxycytidine 5'-diphosphoric acidGenerator
2'-Deoxycytidine diphosphoric acidGenerator
D-1b-Ribofuranosylcytosine diphosphateGenerator
D-1b-Ribofuranosylcytosine diphosphoric acidGenerator
D-1beta-Ribofuranosylcytosine diphosphoric acidGenerator
D-1Β-ribofuranosylcytosine diphosphateGenerator
D-1Β-ribofuranosylcytosine diphosphoric acidGenerator
Deoxycytidine diphosphoric acidGenerator
2'-Deoxy-cytidine 5'-pyrophosphateHMDB
2'-Deoxy-cytidine pyrophosphateHMDB
2'-Deoxycytidine-5'-diphosphateHMDB
4-Amino-1-[2-deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-beta-D-erythro-pentofuranosyl]-2(1H)-pyrimidinoneHMDB
4-Amino-1-[2-deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-beta-delta-erythro-pentofuranosyl]-2(1H)-pyrimidinoneHMDB
delta-1beta-Ribofuranosylcytosine diphosphateHMDB
Deoxy-CDPHMDB
Deoxycytidine 5'-diphosphateHMDB
Chemical FormulaC9H15N3O10P2
Average Molecular Weight387.177
Monoisotopic Molecular Weight387.023266739
IUPAC Name[({[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional NamedCDP
CAS Registry Number800-73-7
SMILES
NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O1
InChI Identifier
InChI=1S/C9H15N3O10P2/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(21-8)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChI KeyFTDHDKPUHBLBTL-SHYZEUOFSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganic oxoanionic compounds
Sub ClassOrganic pyrophosphates
Direct ParentOrganic pyrophosphates
Alternative Parents
Substituents
  • Organic pyrophosphate
  • Aminopyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Imidolactam
  • Alkyl phosphate
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic nitrogen compound
  • Amine
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect

Adverse health effect

Disposition

Biological location

Source

Route of exposure

Process

Naturally occurring process

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Spectral Properties

Experimental Collision Cross Sections

PredictorAdduct TypeData SourceCCS Value (Å2)Reference
AllCCS[M-H]-Not Available172.9http://allccs.zhulab.cn/database/detail?ID=AllCCS00000387
AllCCS[M+H]+Not Available172.1http://allccs.zhulab.cn/database/detail?ID=AllCCS00000387
Predicted Molecular Properties
PropertyValueSource
Water Solubility11.3 g/LALOGPS
logP10(-1.5) g/LALOGPS
logP10(-2.6) g/LChemAxon
logS10(-1.5) g/LALOGPS
pKa (Strongest Acidic)1.79ChemAxon
pKa (Strongest Basic)0.3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area201.44 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity74.78 m³·mol⁻¹ChemAxon
Polarizability30.77 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Spectral Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+182.13431661259
DarkChem[M-H]-177.41131661259
AllCCS[M+H]+179.46332859911
AllCCS[M-H]-173.1932859911

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
dCDP,1TMS,#1C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(N)=NC2=O)O[C@@H]1COP(=O)(O)OP(=O)(O)O3277.7Semi standard non polarhttps://arxiv.org/abs/1905.12712
dCDP,1TMS,#2C[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)C[C@@H]1O)OP(=O)(O)O3323.2Semi standard non polarhttps://arxiv.org/abs/1905.12712
dCDP,1TMS,#3C[Si](C)(C)OP(=O)(O)OP(=O)(O)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)C[C@@H]1O3311.8Semi standard non polarhttps://arxiv.org/abs/1905.12712
dCDP,1TMS,#4C[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O)[C@@H](COP(=O)(O)OP(=O)(O)O)O2)C=C13340.8Semi standard non polarhttps://arxiv.org/abs/1905.12712
dCDP,1TBDMS,#1CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(N)=NC2=O)O[C@@H]1COP(=O)(O)OP(=O)(O)O3528.8Semi standard non polarhttps://arxiv.org/abs/1905.12712
dCDP,1TBDMS,#2CC(C)(C)[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)C[C@@H]1O)OP(=O)(O)O3564.6Semi standard non polarhttps://arxiv.org/abs/1905.12712
dCDP,1TBDMS,#3CC(C)(C)[Si](C)(C)OP(=O)(O)OP(=O)(O)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)C[C@@H]1O3552.8Semi standard non polarhttps://arxiv.org/abs/1905.12712
dCDP,1TBDMS,#4CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O)[C@@H](COP(=O)(O)OP(=O)(O)O)O2)C=C13610.6Semi standard non polarhttps://arxiv.org/abs/1905.12712
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - dCDP GC-MS (Non-derivatized) - 70eV, Positivesplash10-002e-7912000000-ef0991eaee32b505e0162017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - dCDP GC-MS (1 TMS) - 70eV, Positivesplash10-0006-9851100000-62426a0730b483cea09b2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - dCDP GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - dCDP GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - dCDP LC-ESI-QTOF , negative-QTOFsplash10-0570-9418000000-2d9af3073a3dc2deba5d2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - dCDP , negative-QTOFsplash10-056r-9511000000-84defb0c7de79c169ebf2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - dCDP LC-ESI-QTOF , positive-QTOFsplash10-000i-0409000000-e5af2ab8466aa7c560d32017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - dCDP LC-ESI-QTOF , positive-QTOFsplash10-0a4i-0903000000-1de5fa4ac24e19830f392017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - dCDP 10V, Negative-QTOFsplash10-000i-0009000000-4aa3ce1bf37251d7fc832021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - dCDP 20V, Negative-QTOFsplash10-056r-9435000000-55592321586c623c48302021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - dCDP 30V, Positive-QTOFsplash10-0a4i-0903000000-1de5fa4ac24e19830f392021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - dCDP 35V, Negative-QTOFsplash10-056r-9411000000-84bbde6c497548c746d12021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - dCDP 40V, Negative-QTOFsplash10-004i-9100000000-63f9c6b289fb024c58fa2021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dCDP 10V, Positive-QTOFsplash10-03di-0900000000-e584f4f2cb1a8a01a7e72015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dCDP 20V, Positive-QTOFsplash10-03di-3910000000-d34603d21a6d1d52ae1f2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dCDP 40V, Positive-QTOFsplash10-03di-5900000000-52ac41f181e1d5fbf96a2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dCDP 10V, Negative-QTOFsplash10-000f-4209000000-ea241dab90201ce7963e2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dCDP 20V, Negative-QTOFsplash10-004i-9601000000-55120f468bf1ebba66cd2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dCDP 40V, Negative-QTOFsplash10-004i-9100000000-bd81788fb13a599a4f602015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dCDP 10V, Positive-QTOFsplash10-03di-0900000000-63028e00ccb9887f46f52021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dCDP 20V, Positive-QTOFsplash10-03di-1900000000-9b943638c706a10be8db2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dCDP 40V, Positive-QTOFsplash10-03di-3910000000-f5ebfcca0e4ec5d76afa2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dCDP 10V, Negative-QTOFsplash10-000i-0409000000-47d71d5707b30d7b3ad52021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dCDP 20V, Negative-QTOFsplash10-004i-9324000000-25bfbc45e3248b83b2192021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dCDP 40V, Negative-QTOFsplash10-004i-9000000000-a5e502a2627af2048a1f2021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Mitochondria
  • Nucleus
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022510
KNApSAcK IDNot Available
Chemspider ID132961
KEGG Compound IDC00705
BioCyc IDDCDP
BiGG ID50858
Wikipedia LinkDeoxycytidine_diphosphate
METLIN ID6105
PubChem Compound150855
PDB IDNot Available
ChEBI ID28846
Food Biomarker OntologyNot Available
VMH IDDCDP
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNara, Takashi; Misawa, Masanaru. Bacterial phosphorylation of 5'-deoxycytidine monophosphate to di-or triphosphate. Jpn. Tokkyo Koho (1971), 2 pp.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Chiu TH, Morimoto H, Baker JJ: Biosynthesis and characterization of phosphatidylglycerophosphoglycerol, a possible intermediate in lipoteichoic acid biosynthesis in Streptococcus sanguis. Biochim Biophys Acta. 1993 Feb 24;1166(2-3):222-8. [PubMed:8443240 ]

Only showing the first 10 proteins. There are 15 proteins in total.

Enzymes

General function:
Involved in ATP binding
Specific function:
Catalyzes specific phosphoryl transfer from ATP to UMP and CMP.
Gene Name:
CMPK1
Uniprot ID:
P30085
Molecular weight:
20180.12
Reactions
Adenosine triphosphate + dCMP → ADP + dCDPdetails
General function:
Involved in ATP binding
Specific function:
Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4-thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)-benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5-methylcytidine, and N(4)-anisoylcytidine.
Gene Name:
UCK1
Uniprot ID:
Q9HA47
Molecular weight:
22760.43
Reactions
dCTP + Uridine → dCDP + Uridine 5'-monophosphatedetails
dCTP + Cytidine → dCDP + Cytidine monophosphatedetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP (By similarity).
Gene Name:
NME4
Uniprot ID:
O00746
Molecular weight:
20658.45
Reactions
Adenosine triphosphate + dCDP → ADP + dCTPdetails
General function:
Involved in oxidation reduction
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.
Gene Name:
RRM1
Uniprot ID:
P23921
Molecular weight:
90069.375
Reactions
dCDP + Thioredoxin disulfide + Water → Thioredoxin + CDPdetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. Possesses nucleoside-diphosphate kinase, serine/threonine-specific protein kinase, geranyl and farnesyl pyrophosphate kinase, histidine protein kinase and 3'-5' exonuclease activities. Involved in cell proliferation, differentiation and development, signal transduction, G protein-coupled receptor endocytosis, and gene expression. Required for neural development including neural patterning and cell fate determination.
Gene Name:
NME1
Uniprot ID:
P15531
Molecular weight:
17148.635
Reactions
Adenosine triphosphate + dCDP → ADP + dCTPdetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate.
Gene Name:
NME7
Uniprot ID:
Q9Y5B8
Molecular weight:
42491.365
Reactions
Adenosine triphosphate + dCDP → ADP + dCTPdetails
General function:
Involved in oxidoreductase activity
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. Inhibits Wnt signaling.
Gene Name:
RRM2
Uniprot ID:
P31350
Molecular weight:
44877.25
Reactions
dCDP + Thioredoxin disulfide + Water → Thioredoxin + CDPdetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. Negatively regulates Rho activity by interacting with AKAP13/LBC. Acts as a transcriptional activator of the MYC gene; binds DNA non-specifically (PubMed:8392752). Exhibits histidine protein kinase activity.
Gene Name:
NME2
Uniprot ID:
P22392
Molecular weight:
30136.92
Reactions
Adenosine triphosphate + dCDP → ADP + dCTPdetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. Probably has a role in normal hematopoiesis by inhibition of granulocyte differentiation and induction of apoptosis.
Gene Name:
NME3
Uniprot ID:
Q13232
Molecular weight:
19014.85
Reactions
Adenosine triphosphate + dCDP → ADP + dCTPdetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. Inhibitor of p53-induced apoptosis.
Gene Name:
NME6
Uniprot ID:
O75414
Molecular weight:
22002.965
Reactions
Adenosine triphosphate + dCDP → ADP + dCTPdetails

Only showing the first 10 proteins. There are 15 proteins in total.